We examined the natural population structure of the Turkish hamster (Mesocricetus brandti) by analysing partial mitochondrial sequences of the control region and the cytochrome b gene. Evolutionary lineages were defined on haplotype clusters in genetic trees and a median-joining network. Most significant divergence events in M. brandti nested in the lower Pleistocene. Gene flow prevented spatial genetic differentiation among most populations contrasting previous ideas about potential subspeciation in Anatolia. None of the mitochondrial lineages showed significant signs of recent expansion indicating relatively stable ecological conditions during recent population history. Furthermore, we discussed aspects of the evolution of M. brandti and the genus Mesocricetus in the context of available fossils.